KMC hangs

[jodyphelan]

I am running kmc off a fastq file and mostly it runs ok. However, sometimes it hangs for no apparent reason. The command I am running is:

kmc -v -sm -m8 -t2 -sf2 -sp2 -sr2 -k25 @fc1f8619-bc09-460b-b29b-7e490eb0c188.list out .

The c1f8619-bc09-460b-b29b-7e490eb0c188.list file contains the following output:

./1b33b732-1720-4e18-8e1c-d9de4c78a87d.spacers.fq.txt

Usually it completes in about two seconds, but occasionally it will just indefinitely hang. Here are the reads I am running it on: 1b33b732-1720-4e18-8e1c-d9de4c78a87d.spacers.fq.txt

This is the output:

********** Used parameters for Stage 1 : **********
No. of input files           : 1
Output file name             : 
No. of working directories   : 1
Input format                 : FASTQ
Output format                : KMC

k-mer length                 : 25
Max. k-mer length            : 256
Signature length             : 9
Both strands                 : true
RAM only mode                : false

******* Stage 1 configuration: *******

No. of bins                  : 512
Bin part size                : 65536
Input buffer size            : 12582912

No. of readers               : 2
No. of splitters             : 2

Max. mem. size               :  8000MB
Max. mem. per storer         :  3934MB
Max. mem. for single package :    15MB

Max. mem. for PMM (bin parts):  6052MB
Max. mem. for PMM (FASTQ)    :  1264MB
Max. mem. for PMM (reads)    :     2MB
Max. mem. for PMM (b. reader):   679MB

Stage 1: 100%
                                                                                                                                                                                      
********** Used parameters for Stage 2 : **********
Min. count threshold         : 2
Max. count threshold         : 1000000000
Max. counter value           : 255

******* Stage 2 configuration: *******
No. of threads               : 2

Max. mem. for 2nd stage      :    16MB

Stage 2: 100%

[jodyphelan]

Just to follow up, if I leave out the -sm flag it seems to be ok (tested with 1000 iterations)